EE2.0.1 Market Issue

I ran EE2.0 for a while without any issues, but decided to flash to 2.0.1 yesterday. That afternoon I downloaded a couple of apps, but this morning I went to check email and take a look at the app store and it says "The linked Program is no longer installed on your phone." What's going on?

I can't really answer all your questions, but didn't want you to think no one was listening

This seems to happen after flashing a ROM that has app2sd. I'm assuming you partitioned your sd card to use a2sd...After partitioning all of the apps are moved to the partition, and market doesn't register as a core app so it moves, too. (Again, if anyone out there has more info, feel free to jump in!)
If (hopefully) you made a nandroid backup before slashing 2.0.1, your best bet will probably be to restore that. That should take you back to 2.0, then reflash 2.0.1.
Assuming you're backing up as you go, there really shouldn't be any harm in doing this, of course everything's at your own risk. The partition will remain after reflashing .0.1, and you can use the ls -l /data command in adb shell to verify a2sd is working. If it is, you should see, "app -> /system/sd/app
app-private -> /system/sd/app-private" in there respective lines.